XSym'09 at VLDB'09 in Lyon, 24 Aug 2009, organised by Zohra Bellahsene (LIRMM Montpellier), Michael Rys (Microsoft), Rainer Unland (Duisburg-Essen) and myself, to be published as LNCS 5679.

Research and Teaching

Ela's research focuses on algorithms, databases, and visualisation. Her main interest is database indexing for DNA, proteins, pathways and networks, ontologies, and text. She is active in XML and data integration. Ela is always looking for graduates who would like to participate in her current or future research projects. Please contact her with a CV and a project outline, and also apply to the graduate school. Ela currently teaches System Analysis, Database Systems Development and E-Commerce.

Recent/Accepted Papers

J. Jakubowska, E. Hunt and M. Chalmers: VisGenome with CartoonPlus: Supporting Large Scale Genomic Analyses via Physical Space Deformation, Future Generation Computer Systems, to appear
S. Fairley, J. D. McClure, N. Hanlon, R. Irving, M. W. McBride, A. F. Dominiczak and E. Hunt: Mapping Affymetrix Microarray Probes to the Rat Genome via a Persistent Index, International Journal of Knowledge Discovery in Bioinformatics (IJKDB), to appear
N. Anwar and E. Hunt: Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies, BMC Bioinformatics, to appear
N. Anwar and E. Hunt: Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment, BMC Evolutionary Biology 2009, 9:93 doi:10.1186/1471-2148-9-93, pdf
C. Sturm, E. Hunt and M. H. Scholl: Distributed Privilege Enforcement in PACS, DBSec'09, Montreal, Canada, July  2009, LNCS 5645, 142-158, pdf.
T. Bocek, F. V. Hecht, D. Hausheer, E. Hunt and B. Stiller: Mobile P2P Fast Similarity Search (demo), CCNC 2009, Las Vegas, USA, Jan 2009, report and paper.
N. Anwar, E. Hunt, W. Kolch and A. Pitt: Semantic Data Integration for Francisella  tularensis novicida Proteomic and Genomic Data. SWAT4LS, Edinburgh, UK, Nov 2008, the slides and paper, paper at CEUR (vol 435), blog entry.

Recent Grants

Royal Society travel grant for research at the ETH Zurich, July-Aug 2009

Publications  >     Editorial Work   >      Peer Review and Organisation   >

PhD Supervision and Collaborations

Martin Goodfellow, PhD student in graph merging and splitting, with application to systems biology and the web, EPSRC funded (DTA)
Collaboration with Nadia Anwar in semantic data intergration for biology
Collaboration with Thomas Bocek, Fabio Hecht, and Burkhard Stiller of the University of Zurich in fast approximate searching, with application to P2P and mobile devices, FastSS
Collaboration with Zohra Bellahsene at LIRMM, Montpellier
Collaboration with Christoph Sturm, the University of Zurich
Last year I worked in semantic data integration with Patrick Ziegler of the University of Zurich.

Talks and Demos

(1) VLDB'07 demo POSTER. (2) BioXMash, Sept 2007, a one-page summary, and a blog comment. (3) A public lecture at NeSC Edinburgh, May 2008. >>, view webcast. (4) DILS'08: demo and flash presentation SemanticBioXMash, and demo, paper presentation and poster on scaling and user studies with VisGenome. (5) Roslin Institute, Jan 2009, GoogleMaps and MashUps for Genomes: slides.

Software

GeneGram is a genome indexing GUI, currently being developed by Martin Goodfellow.  It is based on software developed by Susan Fairley - mapping microarray probes to the rat genome, in Java and SQL, designed and implemented by Susan at Glasgow. It supports the creation of an n-gram index to the rat genome, and exhaustive matching on that sequence for Affymetrix microarray probes.
VisGenome shows single and comparative representations of the human, mouse and rat genomes. Executables, source code and the User Manual are available.
Fast Similarity Search (FastSS), see a poster summary, performs an exhaustive similarity search in a dictionary, based on the edit distance model of string similarity. The algorithm uses deletions of the human, mouse and rat genomes. Executables, source code and the User Manual are available.ns to model the edit distance.
XBenchMatch is a schema matching benchmark for XML.
1996-98 I build a database and an integrated map for the human chromosome 21

Past PhD Students 

Joanna Jakubowska PhD, Usability of genome browsers, 2008, now working for IBM in Krakow.
Nadia Anwar PhD, Taxonomy-aware querying in a phylogenetic database, 2008, now moving to Memorial Sloan-Kettering Cancer Center.
Susan Fairley PhD, Micro array probe mapping for the rat Affymetrix chip, using a relational index to the rat genome, 2007, now at Ensembl.
Andy Jones PhD, Data standards for functional genomics, 2005, now lecturer at Liverpool, Proteomics and Functional Genomics Group, the Faculty of Veterinary Science.

All Past Students   >

Personal Background

Ela comes from Poland where she graduated in English from the Jagiellonian University of Krakow (MA thesis on Mervyn Peake). She then obtained further qualifications in Scottish Literature (MPhil thesis on John Galt) and Computing Science (BA and Diploma in Computing, OU), with a PhD in Computing from the University of Glasgow in 2002 on the creation of very large disk-based suffix trees. She worked at the Jagiellonian University of Krakow as lecturer in English, at BP Exploration in Scotland and Max Planck Institute for Molecular Genetics in Berlin as software analyst, and at the University of Glasgow in Scotland as Polish lector and a research fellow in computing science. Recently, she was an Oberassistentin in the Database Technology Research Group led by Klaus R. Dittrich at the University of Zurich, and then a Marie-Curie Fellow at the Swiss Federal Institute of Technology in Zurich (ETH Zurich) in the Global Information Systems Group led by Moira Norrie. Beside research, she enjoys skiing and hillwalking.

Updated in July 2009, www.cis.strath.ac.uk/~ela

VG demo - please email me to get the demo